the bioinformatics chat

#39 Amplicon sequence variants and bias with Benjamin Callahan


Listen Later

In this episode, Benjamin Callahan talks about some of the issues faced by

microbiologists when conducting amplicon sequencing and metagenomic studies. The two main themes are:

  • Why one should probably avoid using OTUs (operational taxonomic units) and
  • use exact sequence variants (also called amplicon sequence variants, or
    ASVs), and how DADA2 manages to deduce the exact sequences present in the
    sample.
  • Why abundances inferred from community sequencing data are biased, and
  • how we can model and correct this bias.

    Links:

    • Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (Benjamin J Callahan, Paul J McMurdie & Susan P Holmes)
    • DADA2: High-resolution sample inference from Illumina amplicon data (Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson & Susan P Holmes)
    • In Nature, There Is Only Diversity (Michael R. McLaren, Benjamin J. Callahan)
    • Consistent and correctable bias in metagenomic sequencing experiments (Michael R McLaren, Amy D Willis, Benjamin J Callahan)
    • If you enjoyed this episode, please consider supporting the podcast on Patreon.

      ...more
      View all episodesView all episodes
      Download on the App Store

      the bioinformatics chatBy Roman Cheplyaka

      • 4.8
      • 4.8
      • 4.8
      • 4.8
      • 4.8

      4.8

      34 ratings


      More shows like the bioinformatics chat

      View all
      Radiolab by WNYC Studios

      Radiolab

      43,909 Listeners

      This American Life by This American Life

      This American Life

      90,830 Listeners

      The Bioinformatics and Beyond Podcast by Leo Elworth

      The Bioinformatics and Beyond Podcast

      10 Listeners

      If Books Could Kill by Michael Hobbes & Peter Shamshiri

      If Books Could Kill

      8,747 Listeners

      the bioinformatics lab by The Bioinformatics Lab

      the bioinformatics lab

      0 Listeners